My Thinkpad has no Windows key, so I was using a startup file with xmodmap commands to map my right alt to the Windows key (Super_L).
That worked great until I updated Debian to Squeeze. Then it would only work if I ran it manually after Gnome came up. I tried several startup scripts with different names including .gnomerc, but my settings just wouldn't stick.
So I decided it must be getting overridden by a later step, probably a step where it checks gnome-keyboard-properties settings and calls setxkbmap, so that resets anything you tried to do in a start-up script.
There is an option in gnome-keyboard-properties for "Left Alt is swapped with Left Win". That causes it to run setxkbmap -option altwin:swap_lalt_lwin I believe. That would work perfectly for me, except I want to map the right alt, not the left alt.
So finally, here is what I came up with (probably not the right solution, but it works). I edited all the files in /usr/share/X11/xkb/rules/ with swap_lalt_lwin in them and added a similar line/section called swap_ralt_lwin. Similarly I edited /usr/share/X11/xkb/symbols/altwin and added a section at the bottom for swap_ralt_lwin that works similar to the swap_lalt_lwin section.